Re: [ccp4bb] Calculating volume of Ligands

ccp4 includes a program called 'volume' that does this. see 'man volume' for a description, or $CCP4/html/volume.html Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 15 Jan 2008, Rajan Pillai wrote: Hi All, Can anyone tell

Re: [ccp4bb] crystallisation robot

Dear Alexey, being involved in the development of the 'fixed needles + a few' robots and 96-well plates early on, I wonder about your bad experiences. You seem to say that the Phoenix requires more maintenance than the Mosquito - how long have you had that Phoenix or what model is giving you

[ccp4bb] Calculating volume of Ligands

Hi All, Can anyone tell me any program that calculates voume of a ligand? Moreover, is there also any program that can calculate the volume of a ligand from its coordinates? Thanks, Rajan.

Re: [ccp4bb] CCP4 workshop in US, 2nd announcement

The workshop will be held from May 23 through 28, 2008. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT, Bld. 436, D007 Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 [EMAIL PROTECTED] ___

[ccp4bb] CCP4 workshop in US, 2nd announcement

Dear Colleagues, This is second announcement of the CCP4 workshop. WHAT "CCP4 school: From data processing to structure refinement and beyond". WHERE Advanced Photon Source, Argonne National Laboratory, near Chicago, USA. ORGANIZERS CCP4, University of York, GM/CA-CAT Argonne PROGRAM Lec

Re: [ccp4bb] Perl

Hi, thanks for all the help! system ("source ccp4.setup") does the trick, every time before a ccp4 script is called, the environmental parameters have to be set up this way. Quoting Ed Hoeffner <[EMAIL PROTECTED]>: > Hi > > You don't include any error messages, so it's very difficult to > tr

[ccp4bb] Post-doctoral/Research Associate Position Available

NIH Funded position for studies on studies on the yeast ATP synthase. Studies on mutant forms of the F1 ATPase and on the F1­Fo ATP synthase. The candidate must have a PhD, or the equivalent, with research experience in Biochemistry, Biophysics, Structural Biology, or Molecular Biology. See: htt

Re: [ccp4bb] wich program to test an alternative phaser solution

As suggested earlier, you can use the TOPFILES command to get Phaser to produce the files for more solutions. However, instead of rerunning the whole job, you can produce the PDB files alone by feeding the .sol file into a packing (MR_PAK) job, or both PDB and MTZ files by feeding the .sol file

Re: [ccp4bb] PERL system call to CCP4

Hi, Here is a copy of the occp4.pm file which we use at the PDB Depositions and Processing Site at the EBI. This perl module works and can be called as following: #/bin/perl require '/ebi/msd/work2/msdsd/production/x86_64/lib/site_perl/occp4.pm'; my $sfcheck = new occp4('sfcheck','hklin'=>$sf

Re: [ccp4bb] raid array load comments

Harry M. Greenblatt schrieb: BS"D Thank you to all the respondents. Some comments: 1. Some believe that the write performance in RAID 5 is only as good as I'm one of those "some" (based on experience, and a basic understanding of how RAID5 operates). Even 3ware gives performance data fo

Re: [ccp4bb] wich program to test an alternative phaser solution

Alternatively, ask Phaser to output pdb and mtz files for both solutions with TOPFILES 2 Airlie On Jan 15 2008, Eleanor Dodson wrote: PDBSET xyzin model.pdb ROTA EULER a b c SHIFT FRAC tx ty tz CELL new cell end Vellieux wrote: Dear all, We have a phaser output with 2 alternative solutions

Re: [ccp4bb] crystallization robot

Madhavi Although the Douglas robots are generally cheaper, we think they beat all other robots in several areas: 1. All of the Oryx systems waste virtually no protein - you would set up a (100 + 100 nl) sitting drop plate with only 9.8 microlitres of protein 2. They are very versatile: simply b

Re: [ccp4bb] wich program to test an alternative phaser solution

Hi Fred, in future PHASER runs you can also ask the program to write out an X number of the top solutions as separate coordinate files via the keyword TOPFILES (e.g 'TOPFILES 10' for the top ten solutions). In the PHASER GUI you can enter that request in the 'Define Data' block. best wishes, Savva

Re: [ccp4bb] wich program to test an alternative phaser solution

PDBSET xyzin model.pdb ROTA EULER a b c SHIFT FRAC tx ty tz CELL new cell end Vellieux wrote: Dear all, We have a phaser output with 2 alternative solutions. Not differing much by the statistics. Phaser provides the solution with the highest LLG. However I am not convinced by that solution.

[ccp4bb] raid array load comments

BS"D Thank you to all the respondents. Some comments: 1. Some believe that the write performance in RAID 5 is only as good as performance to one disk. This is true only in RAID 3 (under certain conditions), where parity is written as a separate operation to one dedicated parity disk. W

[ccp4bb] wich program to test an alternative phaser solution

Dear all, We have a phaser output with 2 alternative solutions. Not differing much by the statistics. Phaser provides the solution with the highest LLG. However I am not convinced by that solution. What program should be used with the input PDB and the Euler angles and translation parameters

Re: [ccp4bb] raid array load question

Woops! Yes, of course you would want an ampersand in my little pseudo-script to background the "dd" jobs. My mistake. "seq" is also one of my favorite commands, but some systems are so stripped-down that they don't have it! -James Tim Gruene wrote: Interesting and simple way to test the wr

Re: [ccp4bb] raid array load question

Interesting and simple way to test the write performance. Simultaneous writes could then be tested by putting an ampersand ('&') at the end of the 'dd' command, couldn't they? And if you get tired of typing all the number, you could use the 'seq' command instead. Cheers, Tim /bin/tcsh set ti